(git:e5fdd81)
input_cp2k_voronoi.F
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1 !--------------------------------------------------------------------------------------------------!
2 ! CP2K: A general program to perform molecular dynamics simulations !
3 ! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4 ! !
5 ! SPDX-License-Identifier: GPL-2.0-or-later !
6 !--------------------------------------------------------------------------------------------------!
7 
8 ! **************************************************************************************************
9 !> \brief function that build the dft section of the input
10 !> \par History
11 !> 10.2005 moved out of input_cp2k [fawzi]
12 !> \author fawzi
13 ! **************************************************************************************************
14 MODULE input_cp2k_voronoi
15  USE bibliography, ONLY: brehm2018,&
16  brehm2020,&
17  brehm2021,&
18  rycroft2009,&
19  thomas2015
20  USE cp_output_handling, ONLY: cp_print_key_section_create,&
21  debug_print_level
22  USE input_constants, ONLY: voro_radii_cov,&
23  voro_radii_unity,&
24  voro_radii_user,&
25  voro_radii_vdw
26  USE input_keyword_types, ONLY: keyword_create,&
27  keyword_release,&
28  keyword_type
29  USE input_section_types, ONLY: section_add_keyword,&
30  section_type
31  USE input_val_types, ONLY: integer_t,&
32  lchar_t,&
33  real_t
34  USE kinds, ONLY: dp
35  USE physcon, ONLY: bohr
36  USE string_utilities, ONLY: s2a
37 #include "./base/base_uses.f90"
38 
39  IMPLICIT NONE
40  PRIVATE
41 
42  CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_voronoi'
43 
44  PUBLIC :: create_print_voronoi_section
45 
46 CONTAINS
47 
48 ! **************************************************************************************************
49 !> \brief Create the print voronoi section
50 !> \param print_key ...
51 !> \author Martin Brehm
52 ! **************************************************************************************************
53  SUBROUTINE create_print_voronoi_section(print_key)
54  TYPE(section_type), POINTER :: print_key
55 
56  TYPE(keyword_type), POINTER :: keyword
57 
58  cpassert(.NOT. ASSOCIATED(print_key))
59 
60  ! Voronoi Integration via LibVori
61  CALL cp_print_key_section_create(print_key, __location__, name="VORONOI", &
62  description="Controls the Voronoi integration of the total electron density"// &
63  " for the computation of electromagnetic moments, see [Thomas2015],"// &
64  " [Brehm2020], and [Brehm2021]"// &
65  " (via LibVori see <https://brehm-research.de/voronoi>).", &
66  print_level=debug_print_level + 1, filename="", &
67  citations=(/rycroft2009, thomas2015, brehm2018, brehm2020, brehm2021/))
68 
69  NULLIFY (keyword)
70  CALL keyword_create(keyword, __location__, name="APPEND", &
71  description="Appends frames to already existing .voronoi file.", &
72  default_l_val=.false., lone_keyword_l_val=.true.)
73  CALL section_add_keyword(print_key, keyword)
74  CALL keyword_release(keyword)
75 
76  CALL keyword_create(keyword, __location__, name="SANITY_CHECK", &
77  description="Performs a sanity check before each Voronoi integration, i.e.,"// &
78  " checks if every grid point is located in exactly one Voronoi cell.", &
79  usage="SANITY_CHECK T", default_l_val=.false., lone_keyword_l_val=.true.)
80  CALL section_add_keyword(print_key, keyword)
81  CALL keyword_release(keyword)
82 
83  CALL keyword_create(keyword, __location__, name="OVERWRITE", &
84  description="Specify this keyword to overwrite any existing ""properties.emp"" file if"// &
85  " it already exists. By default, the data is appended to an existing .emp file.", &
86  usage="OVERWRITE T", default_l_val=.false., lone_keyword_l_val=.true.)
87  CALL section_add_keyword(print_key, keyword)
88  CALL keyword_release(keyword)
89 
90  CALL keyword_create(keyword, __location__, name="SKIP_FIRST", &
91  description="Skips the first step of a MD run (avoids duplicate step if restarted).", &
92  usage="SKIP_FIRST T", default_l_val=.false., lone_keyword_l_val=.true.)
93  CALL section_add_keyword(print_key, keyword)
94  CALL keyword_release(keyword)
95 
96  CALL keyword_create(keyword, __location__, name="VERBOSE", &
97  description="Switches on verbose screen output of the Voronoi integration.", &
98  usage="VERBOSE T", default_l_val=.false., lone_keyword_l_val=.true.)
99  CALL section_add_keyword(print_key, keyword)
100  CALL keyword_release(keyword)
101 
102  CALL keyword_create(keyword, __location__, name="OUTPUT_EMP", &
103  description="Writes the resulting electromagnetic moments to a binary file ""properties.emp""."// &
104  " The file name cannot be changed.", &
105  usage="OUTPUT_EMP T", default_l_val=.false., lone_keyword_l_val=.true.)
106  CALL section_add_keyword(print_key, keyword)
107  CALL keyword_release(keyword)
108 
109  CALL keyword_create(keyword, __location__, name="OUTPUT_TEXT", &
110  description="Writes the resulting electromagnetic moments to text files (*.voronoi)."// &
111  " The file name is specified via FILENAME.", &
112  usage="OUTPUT_TEXT T", default_l_val=.true., lone_keyword_l_val=.true.)
113  CALL section_add_keyword(print_key, keyword)
114  CALL keyword_release(keyword)
115 
116  CALL keyword_create(keyword, __location__, name="REFINEMENT_FACTOR", &
117  description="Sets the refinement factor for the Voronoi integration.", &
118  usage="REFINEMENT 2", n_var=1, default_i_val=1, type_of_var=integer_t)
119  CALL section_add_keyword(print_key, keyword)
120  CALL keyword_release(keyword)
121 
122  CALL keyword_create(keyword, __location__, name="VORONOI_RADII", &
123  description="Which atomic radii to use for the radical Voronoi tessellation.", &
124  usage="VORONOI_RADII {UNITY,VDW,COVALENT,USER}", repeats=.false., n_var=1, &
125  default_i_val=voro_radii_vdw, &
126  enum_c_vals=s2a("UNITY", "VDW", "COVALENT", "USER"), &
127  enum_desc=s2a("Use unity radii (non-radical Voronoi tessellation)", "Use VdW atom radii", &
128  "Use covalent atom radii", "Use user-specified atom radii"), &
129  enum_i_vals=(/voro_radii_unity, voro_radii_vdw, voro_radii_cov, voro_radii_user/))
130  CALL section_add_keyword(print_key, keyword)
131  CALL keyword_release(keyword)
132 
133  CALL keyword_create(keyword, __location__, name="USER_RADII", &
134  description="Defines user atom radii for the radical Voronoi tessellation (one per atom).", &
135  usage="USER_RADII {real} {real} {real}", repeats=.false., &
136  unit_str="angstrom", &
137  type_of_var=real_t, n_var=-1)
138  CALL section_add_keyword(print_key, keyword)
139  CALL keyword_release(keyword)
140 
141  CALL keyword_create(keyword, __location__, name="MOLECULAR_PROPERTIES", &
142  description="Calculation of molecular properties from Voronoi integration.", &
143  usage="MOLECULAR_PROPERTIES T", default_l_val=.false., lone_keyword_l_val=.true.)
144  CALL section_add_keyword(print_key, keyword)
145  CALL keyword_release(keyword)
146 
147  CALL keyword_create(keyword, __location__, name="MOLPROP_FILE_NAME", &
148  description="Root of the file name where to print molecular properties."// &
149  " filename.molprop is used.", &
150  usage="MOLPROP_FILE_NAME <FILENAME>", &
151  default_lc_val="__STD_OUT__", type_of_var=lchar_t)
152  CALL section_add_keyword(print_key, keyword)
153  CALL keyword_release(keyword)
154 
155  CALL keyword_create(keyword, __location__, name="JITTER", &
156  description="The Voronoi tessellation can have issues with highly symmetric structures."// &
157  " This keyword displaces all atoms pseudo-randomly by a tiny amount (see JITTER_AMPLITUDE)"// &
158  " to break symmetry. The displacement is constant over time, so that no temporal noise is"// &
159  " introduced. The displacement is not visible to other CP2k routines (FORCE_EVAL, output)."// &
160  " It is only applied internally in the library for the Voronoi tessellation.", &
161  usage="JITTER T", default_l_val=.true., lone_keyword_l_val=.true.)
162  CALL section_add_keyword(print_key, keyword)
163  CALL keyword_release(keyword)
164 
165  CALL keyword_create(keyword, __location__, name="JITTER_SEED", &
166  description="Sets the random seed for the jitter. The pseudo-random number generator"// &
167  " is re-initialized for each Voronoi tessellation so that the jitter is constant over"// &
168  " simulation time (no temporal noise).", &
169  usage="JITTER_SEED 1234", n_var=1, default_i_val=0, type_of_var=integer_t)
170  CALL section_add_keyword(print_key, keyword)
171  CALL keyword_release(keyword)
172 
173  CALL keyword_create(keyword, __location__, name="JITTER_AMPLITUDE", &
174  description="Sets the maximum displacement amplitude for the jitter.", &
175  usage="JITTER_AMPLITUDE 0.01", unit_str="angstrom", n_var=1, default_r_val=1.e-3_dp*bohr, &
176  type_of_var=real_t)
177  CALL section_add_keyword(print_key, keyword)
178  CALL keyword_release(keyword)
179 
180  END SUBROUTINE create_print_voronoi_section
181 
182 END MODULE input_cp2k_voronoi
bibliography
collects all references to literature in CP2K as new algorithms / method are included from literature...
Definition: bibliography.F:28
bibliography::brehm2021
integer, save, public brehm2021
Definition: bibliography.F:43
bibliography::brehm2020
integer, save, public brehm2020
Definition: bibliography.F:43
bibliography::thomas2015
integer, save, public thomas2015
Definition: bibliography.F:43
bibliography::brehm2018
integer, save, public brehm2018
Definition: bibliography.F:43
bibliography::rycroft2009
integer, save, public rycroft2009
Definition: bibliography.F:43
cp_output_handling
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
Definition: cp_output_handling.F:25
cp_output_handling::debug_print_level
integer, parameter, public debug_print_level
Definition: cp_output_handling.F:73
cp_output_handling::cp_print_key_section_create
subroutine, public cp_print_key_section_create(print_key_section, location, name, description, print_level, each_iter_names, each_iter_values, add_last, filename, common_iter_levels, citations, unit_str)
creates a print_key section
Definition: cp_output_handling.F:174
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition: input_constants.F:17
input_constants::voro_radii_user
integer, parameter, public voro_radii_user
Definition: input_constants.F:637
input_constants::voro_radii_vdw
integer, parameter, public voro_radii_vdw
Definition: input_constants.F:637
input_constants::voro_radii_unity
integer, parameter, public voro_radii_unity
Definition: input_constants.F:637
input_constants::voro_radii_cov
integer, parameter, public voro_radii_cov
Definition: input_constants.F:637
input_cp2k_voronoi
function that build the dft section of the input
Definition: input_cp2k_voronoi.F:14
input_cp2k_voronoi::create_print_voronoi_section
subroutine, public create_print_voronoi_section(print_key)
Create the print voronoi section.
Definition: input_cp2k_voronoi.F:54
input_keyword_types
represents keywords in an input
Definition: input_keyword_types.F:14
input_keyword_types::keyword_release
subroutine, public keyword_release(keyword)
releases the given keyword (see doc/ReferenceCounting.html)
Definition: input_keyword_types.F:426
input_keyword_types::keyword_create
subroutine, public keyword_create(keyword, location, name, description, usage, type_of_var, n_var, repeats, variants, default_val, default_l_val, default_r_val, default_lc_val, default_c_val, default_i_val, default_l_vals, default_r_vals, default_c_vals, default_i_vals, lone_keyword_val, lone_keyword_l_val, lone_keyword_r_val, lone_keyword_c_val, lone_keyword_i_val, lone_keyword_l_vals, lone_keyword_r_vals, lone_keyword_c_vals, lone_keyword_i_vals, enum_c_vals, enum_i_vals, enum, enum_strict, enum_desc, unit_str, citations, deprecation_notice, removed)
creates a keyword object
Definition: input_keyword_types.F:155
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition: input_section_types.F:15
input_section_types::section_add_keyword
subroutine, public section_add_keyword(section, keyword)
adds a keyword to the given section
Definition: input_section_types.F:504
input_val_types
a wrapper for basic fortran types.
Definition: input_val_types.F:14
input_val_types::real_t
integer, parameter, public real_t
Definition: input_val_types.F:41
input_val_types::lchar_t
integer, parameter, public lchar_t
Definition: input_val_types.F:41
input_val_types::integer_t
integer, parameter, public integer_t
Definition: input_val_types.F:41
kinds
Defines the basic variable types.
Definition: kinds.F:23
kinds::dp
integer, parameter, public dp
Definition: kinds.F:34
physcon
Definition of physical constants:
Definition: physcon.F:68
physcon::bohr
real(kind=dp), parameter, public bohr
Definition: physcon.F:147
string_utilities
Utilities for string manipulations.
Definition: string_utilities.F:16